Dr. Philipp Berger

Scientist
Paul Scherrer Institute
Forschungsstrasse 111
5232 Villigen PSI
Suisse
Forschungsstrasse 111
5232 Villigen PSI
Suisse
Téléphone
Courriel
Research by Philipp Berger
Membrane proteins are at the interface between the extracellular space and the cytoplasma of cells. They transmit signals from other cells to the inside enabling cell type specific answers or they transport essential components into the cell. Our group is interested how synthesis, activation, degradation, and recycling of membrane proteins is regulated. We focus on vascular endothelial growth factor receptor-2 (VEGFR-2) and G-protein coupled receptors (GPCRs). We analyze how these proteins are internalized after stimulation and identify the signals which decide if a receptor is recycled or degraded. Monitoring of these processes needs the simultaneous expression of several fluorescently tagged sensors. Therefore, we developed tools for multigene expression in mammalian cells (MultiLabel, MultiPrime). This allows us to express up to five fluorescently tagged proteins from a single plasmid or baculovirus. Pictures of a cell line stably expressing five fluorescently tagged subcellular markers are shown above.
In addition, we also develop image analysis tools to quantify vesicular transport (Squassh, Squassh3C, SquasshAnalyst). These tools allow the segmentation of fluorescence images and the quantification of colocalization between different channels.
Manual and installation package are available here for download:
SquasshAnalyst manual.
SquasshAnalyst.zip.
toy_example.zip.
SquasshAnalyst manual.
SquasshAnalyst.zip.
toy_example.zip.
Representative references
Receptor trafficking
- Ballmer-Hofer, K., Andersson, A.E., Ratcliffe, L.E., and Berger, P. (2011). Neuropilin-1 promotes VEGFR-2 trafficking through Rab11 vesicles thereby specifying signal output. Blood 118, 816-826.
MultiLabel/ MultiPrime
- Kriz, A., Schmid, K., Baumgartner, N., Ziegler, U., Berger, I., Ballmer-Hofer, K., and Berger, P. (2010). A plasmid-based multigene expression system for mammalian cells. Nat Commun 1, 120.
- Mansouri, M., Bellon-Echeverria, I., Rizk, A., Ehsaei, Z., Cianciolo Cosentino, C., Silva, C.S., Xie, Y., Boyce, F.M., Davis, M.W., Neuhauss, S.C., et al. (2016). Highly efficient baculovirus-mediated multigene delivery in primary cells. Nat Commun 7, 11529.
Squassh, Squassh3C, SquasshAnalyst
- Rizk, A., Paul, G., Incardona, P., Bugarski, M., Mansouri, M., Niemann, A., Ziegler, U., Berger, P., and Sbalzarini, I.F. (2014). Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature protocols 9, 586-596.
- Rizk, A., Mansouri, M., Ballmer-Hofer, K., and Berger, P. (2015). Subcellular object quantification with Squassh3C and SquasshAnalyst. BioTechniques 59, 309-312.
Publications
2011-2020
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Haider RS, Wilhelm F, Rizk A, Mutt E, Deupi X, Peterhans C, et al.
Arrestin-1 engineering facilitates complex stabilization with native rhodopsin
Scientific Reports. 2019; 9(1): 439 (13 pp.). https://doi.org/10.1038/s41598-018-36881-4
DORA PSI -
Xie Y, Mansouri M, Rizk A, Berger P
Regulation of VEGFR2 trafficking and signaling by Rab GTPase-activating proteins
Scientific Reports. 2019; 9(1): 13342 (12 pp.). https://doi.org/10.1038/s41598-019-49646-4
DORA PSI
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Mansouri M, Berger P
Baculovirus for gene delivery to mammalian cells: past, present and future
Plasmid. 2018; 98: 1-7. https://doi.org/10.1016/j.plasmid.2018.05.002
DORA PSI -
Mansouri M, Berger P
Multigene delivery in mammalian cells: recent advances and applications
Biotechnology Advances. 2018; 36(4): 871-879. https://doi.org/10.1016/j.biotechadv.2018.01.012
DORA PSI
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Baculovirus-based genome editing in primary cells
PLASMID 90, 5 (2017).DOI: 10.1016/j.plasmid.2017.01.003
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Highly efficient baculovirus-mediated multigene delivery in primary cells
NATURE COMMUNICATIONS 7, 11529 (2016).DOI: 10.1038/ncomms11529
2010-2015
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Subcellular object quantification with Squassh3C and SquasshAnalyst
BIOTECHNIQUES 59, (2015).DOI: 10.2144/000114352
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NRP1 Presented in trans to the Endothelium Arrests VEGFR2 Endocytosis, Preventing Angiogenic Signaling and Tumor Initiation
DEVELOPMENTAL CELL 28, 633 (2014).DOI: 10.1016/j.devcel.2014.02.010
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Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh
NATURE PROTOCOLS 9, 586 (2014).DOI: 10.1038/nprot.2014.037
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Strategies for multigene expression in eukaryotic cells
PLASMID 75, 12 (2014).DOI: 10.1016/j.plasmid.2014.07.001
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Coordination of VEGF receptor trafficking and signaling by coreceptors
EXPERIMENTAL CELL RESEARCH 319, 1340 (2013).DOI: 10.1016/j.yexcr.2013.03.008
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Integration of multiple expression cassettes into mammalian genomes in a single step
Protocol Exchange , (2011).DOI: 10.1038/protex.2011.249
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Neuropilin-1 promotes VEGFR-2 trafficking through Rab11 vesicles thereby specifying signal output
BLOOD 118, 816 (2011).DOI: 10.1182/blood-2011-01-328773
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The CMT4B disease-causing proteins MTMR2 and MTMR13/SBF2 regulate AKT signalling
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE 15, 307 (2011).DOI: 10.1111/j.1582-4934.2009.00967.x
2006-2010
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A plasmid-based multigene expression system for mammalian cells
NATURE COMMUNICATIONS 1, 120 (2010).DOI: 10.1038/ncomms1120
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Automated unrestricted multigene recombineering for multiprotein complex production
NATURE METHODS 6, 447 (2009).DOI: 10.1038/nmeth.1326
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Identification of the variant Ala335Val of MED25 as responsible for CMT2B2: molecular data, functional studies of the SH3 recognition motif and correlation between wild-type MED25 and PMP22 RNA levels in CMT1A animal models
NEUROGENETICS 10, 275 (2009).DOI: 10.1007/s10048-009-0183-3
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Anti-Mullerian-hormone-dependent regulation of the brain serine-protease inhibitor neuroserpin
JOURNAL OF CELL SCIENCE 121, 3357 (2008).DOI: 10.1242/jcs.031872
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Mtmr13/Sbf2-deficient mice: an animal model for CMT4B2
HUMAN MOLECULAR GENETICS 16, 2991 (2007).DOI: 10.1093/hmg/ddm257
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Multiprotein Expression Strategy for Structural Biology of Eukaryotic Complexes
STRUCTURE 15, 275 (2007).DOI: 10.1016/j.str.2007.01.016
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Multi-level regulation of myotubularin-related protein-2 phosphatase activity by myotubularin-related protein-13/set-binding factor-2
HUMAN MOLECULAR GENETICS 15, 569 (2006).DOI: 10.1093/hmg/ddi473
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Pathomechanisms of mutant proteins in Charcot-Marie-Tooth disease
NEUROMOLECULAR MEDICINE 8, 217 (2006).DOI: 10.1385/NMM:8:1:217
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Protein complex expression by using multigene baculoviral vectors
NATURE METHODS 3, 1021 (2006).DOI: 10.1038/nmeth983
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Schwann cells and the pathogenesis of inherited motor and sensory neuropathies (Charcot-Marie-Tooth disease)
GLIA 54, 243 (2006).DOI: 10.1002/glia.20386